Superman has two known vulnerabilities: magic and kryptonite. Kryptonite and its effects have been shown pretty convincingly in comics. But, magic is another matter in itself. Does Magic completely eliminate Superman's invulnerability or what? Kingdom Come provides two good examples. Wonder Woman's sword was able to cut Superman's finger. The sword being magical was able to bypass Superman's invulnerability and draw blood. So, conceivably, the sword would have been able to kill him. Another example is when Captain Marvel hits Superman multiple times with the lightning. Superman was severly hurt but not killed. It was magical lightning, so shouldn't his invulnerability been nullified and Superman electrocuted?
I know there are other examples, but it seems that Superman's magic vulnerability is not nearly as severe as Kryptonite. And, it changes depending upon the circumstances. Bring Kryptonite in Superman's presence and he becomes powerless but magic is not nearly as consistent. If I was a Superman villain, I would put more stock in taking him down with Kryptonite than using magic. Superman is even shown to give more respect to Kryptonite than magic. Even red sunlight is more effective, and consistent, than magic.